Obviously, I can't say for sure, but we've had success with Gamestop switching over similar pre-orders for collector's editions of other games.
I saw a post on the forums not too long ago regarding this. They said they actually got a call in saying the Pipboy edition was available and he was allowed to switch over his order. If that person was telling the truth, perhaps there is a chance.
You really should get on the phone with them. Like right now. If I had to guess, I'd say no. It happened to a lot of people that went to their local GameStop and got the same deal. GameStop employees can't guarantee it. The online inventory sold out in less than three hours, and that includes hundreds of GameStop stores. It is possible that they were quick enough to do it for you, but don't get your hopes up.
(Also, GameStop has done that for me in the past, but they told me that they would be unable to make such a request this time around, and I missed out on it because it all happened so fast. I literally went into the store, asked, then left. Less than an hour after I left, the Pip-Boy Editions went up on the website. GameStop didn't call me at all, but I don't blame them because it was my responsibility. I literally called the next day, and they told me.)